1XIW

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.

Arnett, K.L., Harrison, S.C., Wiley, D.C.

(2004) Proc.Natl.Acad.Sci.USA 101: 16268-16273

  • DOI: 10.1073/pnas.0407359101

  • PubMed Abstract: 

    • The alpha/beta T cell receptor complex transmits signals from MHC/peptide antigens through a set of constitutively associated signaling molecules, including CD3-epsilon/gamma and CD3-epsilon/delta. We report the crystal structure at 1.9-A resolution ...

    The alpha/beta T cell receptor complex transmits signals from MHC/peptide antigens through a set of constitutively associated signaling molecules, including CD3-epsilon/gamma and CD3-epsilon/delta. We report the crystal structure at 1.9-A resolution of a complex between a human CD3-epsilon/delta ectodomain heterodimer and a single-chain fragment of the UCHT1 antibody. CD3-epsilon/delta and CD3-epsilon/gamma share a conserved interface between the Ig-fold ectodomains, with parallel packing of the two G strands. CD3-delta has a more electronegative surface and a more compact Ig fold than CD3-gamma; thus, the two CD3 heterodimers have distinctly different molecular surfaces. The UCHT1 antibody binds near an acidic region of CD3-epsilon opposite the dimer interface, occluding this region from direct interaction with the TCR. This immunodominant epitope may be a uniquely accessible surface in the TCR/CD3 complex, because there is overlap between the binding site of the UCHT1 and OKT3 antibodies. Determination of the CD3-epsilon/delta structure completes the set of TCR/CD3 globular ectodomains and contributes information about exposed CD3 surfaces.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Howard Hughes Medical Institute, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. arnett@crystal.harvard.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD3 epsilon chain
A, E
105Homo sapiensMutation(s): 0 
Gene Names: CD3E (T3E)
Find proteins for P07766 (Homo sapiens)
Go to Gene View: CD3E
Go to UniProtKB:  P07766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD3 delta chain
B, F
79Homo sapiensMutation(s): 0 
Gene Names: CD3D (T3D)
Find proteins for P04234 (Homo sapiens)
Go to Gene View: CD3D
Go to UniProtKB:  P04234
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
immunoglobulin light chain variable region
C, G
108N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
immunoglobulin heavy chain variable region
D, H
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.874α = 90.00
b = 79.326β = 90.00
c = 150.747γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation